Full wwPDB NMR Structure Validation Report O iPage 3 ullF wwPDB NMR Structure aliVdation Report 2KAV...

Full wwPDB NMR Structure Validation Report iO

May 28, 2020 � 10:25 pm BST

PDB ID : 2KAVTitle : Solution structure of the human Voltage-gated Sodium Channel, brain isoform

(Nav1.2)Authors : Miloushev, V.Z.; Levine, J.A.; Arbing, M.A.; Hunt, J.F.; Pitt, G.S.; Palmer,

A.G.Deposited on : 2008-11-15

This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/NMRValidationReportHelpwith speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)

MolProbity : 4.02b-467Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)

ShiftChecker : 2.11Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.11

https://www.wwpdb.org/validation/2017/NMRValidationReportHelphttps://www.wwpdb.org/validation/2017/NMRValidationReportHelphttps://www.wwpdb.org/validation/2017/NMRValidationReportHelphttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#references

Full wwPDB NMR Structure Validation Report 2KAV

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:SOLUTION NMR

The overall completeness of chemical shifts assignment was not calculated.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

NMR archive(#Entries)

Clashscore 158937 12864Ramachandran outliers 154571 11451

Sidechain outliers 154315 11428

The table below summarises the geometric issues observed across the polymeric chains and their�t to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-de�ned cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions


2 Ensemble composition and analysis iO

This entry contains 15 models. Model 9 is the overall representative, medoid model (most similarto other models). The authors have identi�ed model 1 as representative, based on the followingcriterion: lowest energy.

The following residues are included in the computation of the global validation metrics.

Well-de�ned (core) protein residuesWell-de�ned core Residue range (total) Backbone RMSD (Å) Medoid model

1 A:1791-A:1842, A:1852-A:1865 (66)

0.24 9

Ill-de�ned regions of proteins are excluded from the global statistics.

Ligands and non-protein polymers are included in the analysis.

The models can be grouped into 2 clusters. No single-model clusters were found.

Cluster number Models1 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14

2 10, 12, 13, 15

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#ensemble_composition


3 Entry composition iO

There is only 1 type of molecule in this entry. The entry contains 1667 atoms, of which 816 arehydrogens and 0 are deuteriums.

Molecule 1 is a protein called Sodium channel protein type 2 subunit alpha.

Mol Chain Residues Atoms Trace

1 A 106Total C H N O S1667 544 816 131 170 6

0

There are 23 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 1754 MET - EXPRESSION TAG UNP Q99250A 1755 GLY - EXPRESSION TAG UNP Q99250A 1756 SER - EXPRESSION TAG UNP Q99250A 1757 SER - EXPRESSION TAG UNP Q99250A 1758 HIS - EXPRESSION TAG UNP Q99250A 1759 HIS - EXPRESSION TAG UNP Q99250A 1760 HIS - EXPRESSION TAG UNP Q99250A 1761 HIS - EXPRESSION TAG UNP Q99250A 1762 HIS - EXPRESSION TAG UNP Q99250A 1763 HIS - EXPRESSION TAG UNP Q99250A 1764 SER - EXPRESSION TAG UNP Q99250A 1765 SER - EXPRESSION TAG UNP Q99250A 1766 GLY - EXPRESSION TAG UNP Q99250A 1767 LEU - EXPRESSION TAG UNP Q99250A 1768 VAL - EXPRESSION TAG UNP Q99250A 1769 PRO - EXPRESSION TAG UNP Q99250A 1770 ARG - EXPRESSION TAG UNP Q99250A 1771 GLY - EXPRESSION TAG UNP Q99250A 1772 SER - EXPRESSION TAG UNP Q99250A 1773 HIS - EXPRESSION TAG UNP Q99250A 1774 MET - EXPRESSION TAG UNP Q99250A 1775 ALA - EXPRESSION TAG UNP Q99250A 1776 SER - EXPRESSION TAG UNP Q99250

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#entry_composition


4 Residue-property plots iO

4.1 Average score per residue in the NMR ensemble

These plots are provided for all protein, RNA and DNA chains in the entry. The �rst graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classi�ed as ill-de�ned in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the �nal structure are shown in grey.

• Molecule 1: Sodium channel protein type 2 subunit alpha

Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

M1797

F1798

F1821

L1825

D1826

I1831

A1832

K1833

P1834

N1835

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882

4.2 Scores per residue for each member of the ensemble

Colouring as in section 4.1 above.

4.2.1 Score per residue for model 1


Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

E1792

D1793

D1794

M1797

F1798

F1815

D1820

F1821

A1822

D1823

A1824

L1825

A1832

K1833

P1834

N1835

K1836

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

F1859

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#residue_plots


MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

M1797

F1798

K1817

F1821

A1822

D1823

A1824

L1825

I1831

N1835

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

D1793

D1794

S1819

D1820

F1821

L1825

D1826

I1831

A1832

K1833

P1834

N1835

K1836

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

E1792

M1797

F1798

D1808

A1809

T1810

Q1811

F1812

I1813

I1831

N1835

Q1838

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

L1858

T1862

K1863

R1864

V1865

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

F1798

D1806

T1810

Q1811

D1826

A1832

N1835

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

C1854

A1860

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882




Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

E1792

D1808

F1812

S1819

D1820

F1821

L1825

A1832

K1833

P1834

N1835

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

C1854

L1855

D1856

I1857

L1858

T1862

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

E1792

D1793

D1794

Y1799

W1802

E1803

D1806

P1807

D1808

A1809

E1814

S1819

D1823

D1826

A1832

K1833

P1834

N1835

K1836

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

C1854

L1855

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

E1796

M1797

F1798

Y1799

E1800

D1808

F1821

L1825

D1826

A1832

N1835

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

D1856

F1861

V1865

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882

4.2.9 Score per residue for model 9 (medoid)


Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

M1797

D1806

T1810

F1821

L1825

D1826

P1827

I1831

N1835

L1839

D1843

L1844

P1845

M1846


V1847

S1848

G1849

D1850

R1851

C1854

L1855

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

M1797

F1798

F1805

D1806

E1814

F1815

F1821

L1825

L1830

I1831

A1832

K1833

P1834

N1835

Q1838

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

E1792

D1793

D1794

M1797

F1798

F1812

K1817

D1820

I1831

N1835

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

A1860

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

D1806

T1810

S1819

D1820

F1821

L1825

D1826

L1830

I1831

A1832

K1833

P1834

N1835

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

C1854

L1858

F1859

A1860

F1861

T1862

K1863

R1864

V1865

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882




Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

M1797

D1808

A1809

T1810

Q1811

F1812

S1819

A1832

K1833

P1834

N1835

Q1838

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

F1798

F1805

D1806

Q1811

F1821

A1822

D1823

A1824

L1825

I1831

A1832

K1833

P1834

N1835

Q1838

M1842

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

K1863

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882



Chain A:

MET

GLY

SER

SER

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

ALA

SER

E1777

N1778

F1779

S1780

V1781

A1782

T1783

E1784

E1785

S1786

A1787

E1788

P1789

L1790

S1791

D1794

F1795

D1808

Q1811

F1821

L1825

D1826

L1830

I1831

A1832

K1833

P1834

N1835

D1843

L1844

P1845

M1846

V1847

S1848

G1849

D1850

R1851

I1852

H1853

C1854

F1861

T1862

K1863

R1864

V1865

L1866

G1867

E1868

S1869

G1870

E1871

M1872

D1873

A1874

L1875

R1876

I1877

Q1878

M1879

E1880

E1881

R1882


5 Re�nement protocol and experimental data overview iO

The models were re�ned using the following method: torsion angle dynamics.

Of the 200 calculated structures, 15 were deposited, based on the following criterion: structureswith the lowest energy.

The following table shows the software used for structure solution, optimisation and re�nement.

Software name Classi�cation VersionX-PLOR NIH structure solution 2.18X-PLOR NIH re�nement 2.18

No chemical shift data was provided. No validations of the models with respect to experimentalNMR restraints is performed at this time.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#refinement_protocol


6 Model quality iO

6.1 Standard geometry iO

There are no covalent bond-length or bond-angle outliers.

There are no bond-length outliers.

There are no bond-angle outliers.

There are no chirality outliers.

There are no planarity outliers.

6.2 Too-close contacts iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.

Mol Chain Non-H H(model) H(added) Clashes1 A 543 529 529 11±3All All 8145 7935 7935 167

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 10.

All unique clashes are listed below, sorted by their clash magnitude.

Atom-1 Atom-2 Clash(Å) Distance(Å)Models

Worst Total

1:A:1835:ASN:ND2 1:A:1835:ASN:H 0.72 1.80 10 41:A:1835:ASN:ND2 1:A:1835:ASN:N 0.63 2.47 10 21:A:1835:ASN:N 1:A:1835:ASN:HD22 0.61 1.94 2 3

1:A:1861:PHE:CD2 1:A:1864:ARG:NH2 0.60 2.68 12 11:A:1835:ASN:HD22 1:A:1835:ASN:H 0.60 1.37 9 31:A:1832:ALA:O 1:A:1833:LYS:O 0.59 2.19 13 4

1:A:1831:ILE:HG22 1:A:1835:ASN:OD1 0.59 1.98 11 31:A:1832:ALA:O 1:A:1835:ASN:ND2 0.58 2.37 8 41:A:1861:PHE:O 1:A:1865:VAL:HG22 0.57 1.99 8 2

1:A:1852:ILE:HG22 1:A:1853:HIS:N 0.57 2.15 11 51:A:1835:ASN:H 1:A:1835:ASN:HD22 0.56 1.43 10 11:A:1835:ASN:N 1:A:1835:ASN:ND2 0.56 2.54 9 3

1:A:1835:ASN:HD22 1:A:1835:ASN:N 0.54 1.97 9 11:A:1814:GLU:OE1 1:A:1815:PHE:N 0.54 2.41 10 1

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https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#model_qualityhttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#standard_geometryhttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#close_contacts


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Worst Total

1:A:1852:ILE:HD12 1:A:1852:ILE:N 0.54 2.18 5 21:A:1819:SER:O 1:A:1833:LYS:NZ 0.54 2.41 6 21:A:1861:PHE:CG 1:A:1864:ARG:NH2 0.53 2.75 12 11:A:1803:GLU:OE1 1:A:1803:GLU:N 0.53 2.42 7 11:A:1791:SER:N 1:A:1794:ASP:OD2 0.53 2.42 1 21:A:1806:ASP:O 1:A:1808:ASP:N 0.53 2.43 7 1

1:A:1793:ASP:OD1 1:A:1793:ASP:N 0.53 2.42 11 11:A:1793:ASP:OD1 1:A:1794:ASP:N 0.52 2.42 7 21:A:1800:GLU:N 1:A:1800:GLU:OE1 0.52 2.42 8 11:A:1835:ASN:C 1:A:1835:ASN:HD22 0.52 2.08 14 1

1:A:1802:TRP:CZ3 1:A:1854:CYS:SG 0.52 2.95 7 11:A:1863:LYS:NZ 1:A:1863:LYS:CB 0.51 2.73 6 21:A:1852:ILE:N 1:A:1852:ILE:HD12 0.51 2.20 13 11:A:1835:ASN:O 1:A:1835:ASN:ND2 0.51 2.44 5 21:A:1842:MET:O 1:A:1842:MET:SD 0.50 2.69 1 11:A:1819:SER:OG 1:A:1836:LYS:NZ 0.50 2.42 3 11:A:1792:GLU:H 1:A:1792:GLU:CD 0.50 2.10 6 41:A:1831:ILE:CG2 1:A:1835:ASN:ND2 0.50 2.74 10 21:A:1811:GLN:O 1:A:1854:CYS:SG 0.50 2.70 15 21:A:1838:GLN:O 1:A:1842:MET:SD 0.49 2.70 13 21:A:1826:ASP:N 1:A:1826:ASP:OD1 0.49 2.45 15 1

1:A:1823:ASP:OD2 1:A:1833:LYS:N 0.49 2.46 14 11:A:1861:PHE:CE2 1:A:1864:ARG:NH2 0.48 2.82 12 11:A:1831:ILE:CG2 1:A:1835:ASN:OD1 0.48 2.62 2 31:A:1858:LEU:O 1:A:1862:THR:HG23 0.48 2.09 6 31:A:1834:PRO:O 1:A:1836:LYS:N 0.48 2.45 1 1

1:A:1838:GLN:OE1 1:A:1838:GLN:N 0.48 2.47 10 11:A:1806:ASP:C 1:A:1808:ASP:H 0.48 2.12 7 1

1:A:1826:ASP:OD1 1:A:1826:ASP:N 0.47 2.46 7 21:A:1794:ASP:OD1 1:A:1795:PHE:N 0.47 2.47 15 11:A:1814:GLU:CD 1:A:1814:GLU:N 0.47 2.68 7 11:A:1814:GLU:OE1 1:A:1814:GLU:N 0.47 2.48 7 11:A:1835:ASN:H 1:A:1835:ASN:ND2 0.47 2.07 12 21:A:1821:PHE:CZ 1:A:1825:LEU:HD21 0.47 2.44 10 101:A:1812:PHE:CD2 1:A:1852:ILE:O 0.47 2.68 11 21:A:1791:SER:O 1:A:1794:ASP:OD2 0.46 2.33 15 11:A:1797:MET:C 1:A:1797:MET:SD 0.46 2.94 11 21:A:1797:MET:SD 1:A:1797:MET:C 0.46 2.94 13 31:A:1856:ASP:OD1 1:A:1857:ILE:N 0.46 2.49 6 11:A:1820:ASP:OD1 1:A:1820:ASP:N 0.46 2.49 1 11:A:1832:ALA:O 1:A:1835:ASN:OD1 0.46 2.33 14 2





Worst Total

1:A:1823:ASP:OD2 1:A:1833:LYS:NZ 0.45 2.41 1 11:A:1830:LEU:HD12 1:A:1831:ILE:N 0.45 2.26 10 21:A:1836:LYS:CB 1:A:1836:LYS:NZ 0.45 2.80 7 11:A:1808:ASP:O 1:A:1809:ALA:HB3 0.44 2.12 4 2

1:A:1806:ASP:OD2 1:A:1811:GLN:N 0.44 2.49 5 11:A:1823:ASP:OD1 1:A:1823:ASP:O 0.44 2.35 2 11:A:1853:HIS:O 1:A:1856:ASP:OD2 0.44 2.36 6 11:A:1856:ASP:N 1:A:1856:ASP:OD1 0.44 2.50 8 11:A:1820:ASP:O 1:A:1820:ASP:OD1 0.44 2.36 12 2

1:A:1806:ASP:OD2 1:A:1810:THR:OG1 0.44 2.35 12 21:A:1815:PHE:CD1 1:A:1815:PHE:C 0.43 2.90 1 11:A:1854:CYS:SG 1:A:1855:LEU:N 0.43 2.91 9 11:A:1819:SER:C 1:A:1833:LYS:HZ1 0.43 2.15 13 1

1:A:1823:ASP:OD2 1:A:1831:ILE:O 0.43 2.36 14 11:A:1808:ASP:O 1:A:1808:ASP:OD1 0.43 2.36 8 31:A:1796:GLU:O 1:A:1800:GLU:OE2 0.43 2.37 8 11:A:1826:ASP:OD1 1:A:1827:PRO:O 0.43 2.37 9 11:A:1805:PHE:O 1:A:1806:ASP:OD1 0.43 2.37 14 21:A:1799:TYR:O 1:A:1803:GLU:OE2 0.43 2.36 7 11:A:1806:ASP:OD1 1:A:1810:THR:OG1 0.43 2.37 9 21:A:1852:ILE:CG2 1:A:1853:HIS:N 0.43 2.82 13 31:A:1832:ALA:C 1:A:1833:LYS:O 0.43 2.57 13 21:A:1817:LYS:NZ 1:A:1817:LYS:CB 0.43 2.82 11 11:A:1803:GLU:OE1 1:A:1803:GLU:CA 0.42 2.66 7 11:A:1831:ILE:HD11 1:A:1864:ARG:NH1 0.42 2.29 12 11:A:1798:PHE:C 1:A:1798:PHE:CD1 0.42 2.92 1 41:A:1792:GLU:CD 1:A:1792:GLU:N 0.42 2.72 4 11:A:1819:SER:O 1:A:1823:ASP:OD2 0.42 2.37 7 11:A:1810:THR:O 1:A:1811:GLN:CB 0.42 2.66 4 21:A:1798:PHE:CD1 1:A:1798:PHE:C 0.42 2.92 10 41:A:1831:ILE:CG2 1:A:1838:GLN:NE2 0.41 2.83 4 11:A:1853:HIS:O 1:A:1855:LEU:N 0.41 2.53 6 11:A:1859:PHE:O 1:A:1862:THR:OG1 0.41 2.37 12 11:A:1797:MET:SD 1:A:1826:ASP:OD1 0.41 2.79 9 11:A:1808:ASP:OD1 1:A:1808:ASP:N 0.41 2.51 15 11:A:1811:GLN:O 1:A:1853:HIS:CD2 0.41 2.73 14 1

1:A:1852:ILE:HG22 1:A:1853:HIS:H 0.40 1.75 13 11:A:1855:LEU:CD2 1:A:1855:LEU:N 0.40 2.84 7 11:A:1825:LEU:O 1:A:1830:LEU:HD13 0.40 2.16 12 1


6.3 Torsion angles iO

6.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 66/129 (51%) 61±1 (93±2%) 4±1 (6±2%) 1±1 (1±1%) 20 68All All 990/1935 (51%) 917 (93%) 63 (6%) 10 (1%) 20 68

All 6 unique Ramachandran outliers are listed below. They are sorted by the frequency of occur-rence in the ensemble.

Mol Chain Res Type Models (Total)1 A 1833 LYS 41 A 1832 ALA 21 A 1842 MET 11 A 1807 PRO 11 A 1854 CYS 11 A 1834 PRO 1

6.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 59/112 (53%) 56±1 (95±2%) 3±1 (5±2%) 30 79All All 885/1680 (53%) 843 (95%) 42 (5%) 30 79

All 22 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 1835 ASN 91 A 1826 ASP 71 A 1833 LYS 41 A 1842 MET 2


https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#torsion_angleshttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#protein_backbonehttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#protein_sidechains



Mol Chain Res Type Models (Total)1 A 1852 ILE 21 A 1797 MET 21 A 1811 GLN 11 A 1854 CYS 11 A 1817 LYS 11 A 1855 LEU 11 A 1820 ASP 11 A 1838 GLN 11 A 1819 SER 11 A 1800 GLU 11 A 1839 LEU 11 A 1863 LYS 11 A 1859 PHE 11 A 1814 GLU 11 A 1853 HIS 11 A 1803 GLU 11 A 1793 ASP 11 A 1794 ASP 1

6.3.3 RNA iO

There are no RNA molecules in this entry.

6.4 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

6.5 Carbohydrates iO

There are no carbohydrates in this entry.

6.6 Ligand geometry iO

There are no ligands in this entry.

6.7 Other polymers iO

There are no such molecules in this entry.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#rnahttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp#nonstandard_residues_and_ligands


6.8 Polymer linkage issues iO

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#polymer_linkage


7 Chemical shift validation iO

No chemical shift data were provided

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#chemical_shifts

Overall quality at a glanceEnsemble composition and analysisEntry compositionResidue-property plotsAverage score per residue in the NMR ensembleScores per residue for each member of the ensembleScore per residue for model 1 Score per residue for model 2 Score per residue for model 3 Score per residue for model 4 Score per residue for model 5 Score per residue for model 6 Score per residue for model 7 Score per residue for model 8 Score per residue for model 9 (medoid)Score per residue for model 10 Score per residue for model 11 Score per residue for model 12 Score per residue for model 13 Score per residue for model 14 Score per residue for model 15

Refinement protocol and experimental data overviewModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA

Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues

Chemical shift validation

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